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You can probably hack it quickly by 1- running the preprocessing steps 'background correction', 'normalization' and 'PM correction' on your 'AffyBatch' 2- then running an edited version of the method 'generateExprset.methods.liwong' (returning 'phi' as an attribute for example - see help(attr)). L. > Hi, > I've looked through the archives to see if this question had been > raised before, and not finding anything about it, thought I'd ask. > > I'm wondering if there is a way to get the phi values returned as > output when running expresso with the liwong method settings. Phi > values in the dChip model are the "probe sensitivity index" (PSI). > > I know that expresso just returns the summarized expression value for a > probeset (gene) which is the Theta in the dChip model below: > > PM_ij - v_j = Theta_i*phi_j + e > with v_j a background term. > > If not expresso, are there other functions or methods that can be > tweaked to return the PSI values along with the Theta? If anyone has > tried this before, I'd appreciate your insights. > > Thanks, > Hemali > > Hemali Patel > Department of Biomedical Engineering > Boston University > > > [[alternative text/enriched version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >